Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012359.1 Kokia drynarioides strain JFW-HI SEQ_127361, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27123
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:102 original size:13 final size:13
Alignment explanation
Indices: 86--110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76 AAATTCGGAG
86 TAAAAGCCCGAAT
1 TAAAAGCCCGAAT
99 TAAAAGCCCGAA
1 TAAAAGCCCGAA
111 CCCAATATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (13 bp):
TAAAAGCCCGAAT
Found at i:6418 original size:80 final size:78
Alignment explanation
Indices: 6313--6468 Score: 258
Period size: 80 Copynumber: 2.0 Consensus size: 78
6303 TCATTAAGGA
* * *
6313 GAAATGCCATGCCTTTTAGCTACATCAGATCCTAATGAAGAGACATGACTCATTGGCTTTCCTAC
1 GAAATGCCATGCCTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTAC
6378 AAGAGTTAAAAAC
66 AAGAGTTAAAAAC
*
6391 GAAATTGCCATTCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCT
1 GAAA-TGCCATGCC-TTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCT
6456 ACAAGAGTTAAAA
64 ACAAGAGTTAAAA
6469 TGAAATTAGT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
78 4 0.06
79 8 0.11
80 60 0.83
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (78 bp):
GAAATGCCATGCCTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTAC
AAGAGTTAAAAAC
Found at i:7948 original size:216 final size:216
Alignment explanation
Indices: 7228--10687 Score: 3166
Period size: 216 Copynumber: 16.6 Consensus size: 216
7218 ATTTTCTCGA
* * *
7228 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTTAATTAAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* *
7293 AACTTATTTACGTGAGAATT-ATT-TCTCTTGGTTCTTGGACGAACTTAAGAACTTGTCAAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACTT
* * * * *
7356 TT-TCGAGATCCTTTATTACTTTGATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGA-AAA
131 TTAT-GAGTTCCTTTATAACTTTGGTTCC-TAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
* *
7419 ATTTTCTAAACATTCCATGCTCAG
194 TTTTTC-GAACATTCCATGCTCAG
* * * * * *
7443 AAAATTGAATCATTTTGTCTAAATAGTTTGTCAATTTGTAAACATGTTTTCGTCTTTGAATT--A
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* * * **
7506 AACTCATTCACGTGAGAATTGTTTCTCTCTTGGTTCTGGGATAAACTTCCA-AACTTGTCAAAC-
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT-CAGAACTTGTCAAACT
* * * * *
7569 ---------T--TTT-T--CTTTGGTACCTTAAAGTATTCAAGATGATTCATTCCGTCGAGCAAT
130 TTTATGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
* *
7620 TTTTTGAACATTCCATGCT-TG
195 TTTTCGAACATTCCATGCTCAG
* * * * * *
7641 AAAAATTGTATCATTTGGTCTAAATAGATAGTCATTTTGTAAAAAAG-TTTGTGTCTTTGAATTA
1 -GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTG-GTCTTTGAATTA
* * *
7705 AAAACATATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACGTGTCAAAC
64 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAAC
* * * *
7770 TTTTATGAGTTCCTTTATAACTTTGGTTCCTCAAAGTATTTAAGGCGATCCATTCCTTTGAGCAA
129 TTTTATGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
7835 TTTTTCGAACATTCCATGCTCAG
194 TTTTTCGAACATTCCATGCTCAG
* * * * *
7858 GTAATAGAATCATTTTGTCTAAATAGTTTGTCATTTTGTAAACAGGTTTTGGTCTTTAAATTAAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* * * ***
7923 AACTTATTTATGTGAGAATTGTTTCTCTATTGGTTCTGGGTTAAACTTCCA-AACTTGTCAAACT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT-CAGAACTTGTCAAACT
* * * * *
7987 TTTACT-AATTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATGCATTCCTTCGAGCAA
130 TTTA-TGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
8051 -TTTT----C--T-C--G---A-
194 TTTTTCGAACATTCCATGCTCAG
* * *
8060 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTTAATTAAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* *
8125 AACTTATTTACGTGAGAATTG-TT-TCTCTTGGTTCTTGGACGAACTTAAGAAATTGTCAAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACTT
* * * * * * ** *
8188 TTTTGAGATCTTTTATTACTTTGATTCCTTAAAAGTATTCAAGACGATCCATTCCATC-AAAAAA
131 TTATGAGTTCCTTTATAACTTTGGTTCC-TAAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
* *
8252 TTTTCTGAACATTCCATGCTAAA
195 TTTTC-GAACATTCCATGCTCAG
* * * * * *
8275 AAAATTGAATCATTTTGTCT--A-A---CGTCATTTTGTAAACATGTTTTCGTCTTTGAATT--A
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* * *
8332 AACTCATTCACGTGAGAATTGTTTCTCTCTTGGTTC-TGG--G-A---CA-AACTT-TCGAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACTT
* * * **
8388 GTTA--A---ACTTT-T-ACTTT-GTTACCTTAAAGTATTCAAGACGATCCATTTCTTTAAGCAA
131 -TTATGAGTTCCTTTATAACTTTGGTT-CCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
* * *
8445 TTTCTCGAACATTTCGTGCTCAG
194 TTTTTCGAACATTCCATGCTCAG
* * *
8468 GAAATGGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAG-TTTGTGTCTTTGAATTAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTG-GTCTTTGAATTAA
* * *
8532 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAACTTCTGAACATGTCAAACT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACT
* * * * * *
8597 TTTACGAGTTTCTTTATAACTTTGGTTCCTCAAAGTATTTAAGGCGATCCATTCCTTTGAGCAAT
130 TTTATGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
* *
8662 TTTTCGAACATTTCATGCTCGG
195 TTTTCGAACATTCCATGCTCAG
* * * * *
8684 GTAATCGAATCATTTGGTCTAAATTGTTTGTCATTTTGTAAATAGGTTTTGGTCTTTAAATTAAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* * * * *
8749 AACTTATTTATGTGAGAATTGTTTCTCTATTGGTTCTAGGTCAAACTTCCA-AACTTGTCAAACT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT-CAGAACTTGTCAAACT
* * ** * * * *
8813 TTTACT-AATTCTTTTATAGGTTCGATTCCTTAAAGTATTCAAGACGATGCATTCCTTCGAGCAA
130 TTTA-TGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
*
8877 -ATTT----C--T-C--G---A-
194 TTTTTCGAACATTCCATGCTCAG
* * *
8886 GAAATCGCATCATTTGGTCTAAATAGTTTGTCA-TTTCTAAACAAGTTTTGGTCTTTAAATTAAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
*
8950 AACTTATTTACGTGAGAATTG-TT-TCTCTTGGTTCTTGGACGAACTTAAGAACTTGTCAAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACTT
* * * * *
9013 TT-TCGAGATCTTTTATTACTTTGATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGA--AA
131 TTAT-GAGTTCCTTTATAACTTTGGTTCC-TAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
*
9075 GTTTTTTTGAACATTCCATGCTCAG
194 --TTTTTCGAACATTCCATGCTCAG
* * * * * ***
9100 AAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTAGTAAACATGTTTCCATCTTTGAATT--A
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* * * * *
9163 AACTCATTCACGTGAGAACTGTTTCTCTCTTGGTTCTTGGACGAACTTAAGAAATTGTCAAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACTT
** * * * * * * **
9228 TTACAAGATCCTTTATTACTTCGGTTCCTTAAAAGTATTTAAGACAATCCATTCCTTCAAAAAAA
131 TTATGAGTTCCTTTATAACTTTGGTTCC-TAAAAGTATTCAAGACGATCCATTCCTTC-GAGCAA
** ** * *
9293 AATTT-GAATGTTGCATGCTCGG
194 TTTTTCGAACATTCCATGCTCAG
* * * *
9315 GAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTTGCAAAGATA-TTTTGGTCTTTGAATTAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA-AGTTTTGGTCTTTGAATTAA
* * *
9379 AAACTCATTTACATGAGAATTGTTTCTCTCTTGCTTC-TGG--G-A--T--GAACTT-TCAAACT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACT
* * * *
9435 TGTTA--A---ACTTT-T-ACTTTGGTACCTTAAAGTATTCAAGACGATCCATTCCTTTGAGCAA
130 T-TTATGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
** * *
9493 TTTCCCAAACATTCCGA-GCTCAA
194 TTTTTCGAACATTCC-ATGCTCAG
* *
9516 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAG-TTTGTGTCTTTGAATTAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTG-GTCTTTGAATTAA
* * * *
9580 AAATTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAACTTCTGAACATGTCAAACT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACT
* * * * *
9645 TTTACGAGTTCCTTTATAACTTTGGTTCCTCAAAGTATTTAAGGCGATCCATTCCTTTGAGCAAT
130 TTTATGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
* *
9710 TTTTTGAACATTCCATGCTCGG
195 TTTTCGAACATTCCATGCTCAG
* * *
9732 GTAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAGGTTTTGGTCTTTAAATTAAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
** * * * *
9797 AACTTATTTATATGAGAATTGTTTCTCTATTGGTTCTAGGTCAAACTTCCA-AACTTGTCAAACT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT-CAGAACTTGTCAAACT
* * * * *
9861 TTTACT-AATTCTTTTATAACTTCGGTTCCTAAAAGTATTCAAGATGATACATTCCTTCGAGCAA
130 TTTA-TGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
9925 -TTTT----C--T-C--G---A-
194 TTTTTCGAACATTCCATGCTCAG
* * *
9934 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTTAATTAAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
*
9999 AACTTATTTACGTGAGAATTG-TT-TCTCTTGGTTCTTGGACGAACTTAAGAACTTGTCAAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACTT
* * * *
10062 TT-TCGAGATCCTTTATTACTTTGATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGA--AA
131 TTAT-GAGTTCCTTTATAACTTTGGTTCC-TAAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
*
10124 GTTCTTTTGAACATTCCATGCTCAG
194 -TT-TTTCGAACATTCCATGCTCAG
* * * * * *
10149 AAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTAGTAAACATGTTTTCGTCTTTGAATT--A
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
* * * * *
10212 AACTCATTCACGTGAGAACTGTTTCTCTCTTGGTTCTTGGATGAACTTAAGAACTTGTCAAACTT
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACTT
* * * * * **
10277 TTACGAGATCCTTTATTACTTCGGTTCCTTAAAAGTATTCAAGACGATCCATTCCTTCAAAAAAA
131 TTATGAGTTCCTTTATAACTTTGGTTCC-TAAAAGTATTCAAGACGATCCATTCCTTC-GAGCAA
* ** * *
10342 ATTTT-GAATGTTGCATGCTCGG
194 TTTTTCGAACATTCCATGCTCAG
* * * * *
10364 GAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTTGCAAAGATA-TTTTGGTCTGTGAATTAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA-AGTTTTGGTCTTTGAATTAA
* * * *
10428 AAACTCATTTATGTGAGAATTGTTTCTCTCTTGGTTCTGGGACGAACTTCCGAACTTGTC--A--
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACT
* *
10489 ---A--A----CTTT-T-ACTTTGGTACCTTAAAGTATTCAAGACGATCCATT-CTATCGAGCAA
130 TTTATGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCT-TCGAGCAA
*
10542 -TTTTCTGAACATTCTATGCTCAG
194 TTTTTC-GAACATTCCATGCTCAG
* * * *
10565 GAAATCGCATCATTTGGTCTAAATAGTTTTTAATTTTGTAAAAAAG-TTTGTGTCTTTGAATTAA
1 GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTG-GTCTTTGAATTAA
* * *
10629 AAACTTATTTACGTGAGAATCGTTTCTCTTTTAGTTCTTGGACGAACTTTC-GAACTTGT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC-TTCAGAACTTGT
10688 TAAATGATGC
Statistics
Matches: 2672, Mismatches: 403, Indels: 354
0.78 0.12 0.10
Matches are distributed among these distances:
193 56 0.02
194 14 0.01
195 2 0.00
196 4 0.00
197 1 0.00
198 11 0.00
199 178 0.07
200 177 0.07
201 463 0.17
202 220 0.08
203 6 0.00
204 10 0.00
205 5 0.00
206 6 0.00
207 23 0.01
208 21 0.01
209 68 0.03
210 17 0.01
211 9 0.00
212 1 0.00
213 63 0.02
214 47 0.02
215 503 0.19
216 656 0.25
217 107 0.04
218 4 0.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (216 bp):
GAAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAA
AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCAGAACTTGTCAAACTT
TTATGAGTTCCTTTATAACTTTGGTTCCTAAAAGTATTCAAGACGATCCATTCCTTCGAGCAATT
TTTCGAACATTCCATGCTCAG
Found at i:9365 original size:21 final size:21
Alignment explanation
Indices: 9324--9365 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9314 GGAAATTGAA
*
9324 TCATTTTGTCTAAATAGTTTG
1 TCATTTTGTCAAAATAGTTTG
*
9345 TCATTTTG-CAAAGATATTTTG
1 TCATTTTGTCAAA-ATAGTTTG
9366 GTCTTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (21 bp):
TCATTTTGTCAAAATAGTTTG
Found at i:9842 original size:832 final size:821
Alignment explanation
Indices: 6927--10498 Score: 3890
Period size: 832 Copynumber: 4.3 Consensus size: 821
6917 CGAGCTTCTA
* * * *
6927 AACATGTTAAACTTTTACGAGTTCCTTTAAAACTTTGGATCCTTAAAGTATTCAAGGCGATCCAT
1 AACATGTCAAACTTTTA-GA--TACTTTATAACTTTGGTTCCTTAAAGTATTCAAGGCGATCCAT
* * *
6992 TCCTTCGAGCAATTTTTCAAACATTCCATGCTCGGGTAATTGAATCATTTGGTCTAAATAGTTTG
63 TCCTTTGAGCAATTTTTCGAACATTCCATGCTCGGGTAATCGAATCATTTGGTCTAAATAGTTTG
* * *
7057 TCA-TTTGTAAACAGGTTTTGGTGTTTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTAT
128 TCATTTTGTAAAAAGGTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTAT
* * *
7121 TGGTTCTGGGACGAACTTCTGAACTT-TGCAAACTTTTACTAGTTCTTTTATAACTTCGGTTCCT
193 TGGTTCTGGGATGAACTTCCGAACTTGT-CAAACTTTTACTAATTCTTTTATAACTTCGGTTCCT
**
7185 TAAAGTATTCAAGATAATGCATTCCTTCGAGCAAT---TTTCTCGAGAAATCGCATCATTTGGTC
257 TAAAGTATTCAAGACGATGCATTCCTTCGAGCAATAAATTTCTCGAGAAATCGCATCATTTGGTC
*
7247 TAAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTTAATTAAAAACTTATTTACGTGAGAAT
322 TAAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAAT
* *
7312 TATTTCTCTTGGTTCTTGGACGAACTTAAGAACTTGTCAAACTTTTTCGAGATCCTTTATTACTT
387 TGTTTCTC----TTCTTGGA-GAACTTAAG-A---GTCAAACTTTTTCGAGATCTTTTATTACTT
*
7377 TGATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGAAAAATTTTCTAAACATTCCATGCTCA
443 TGATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGAAAAATTTTCTGAACATTCCATGCTCA
*
7442 GAAAATTGAATCATTTTGTCTAAATAGTTTGTCAATTTGTAAACATGTTTTCGTCTTTGAATTAA
508 GAAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTTGTAAACATGTTTTCGTCTTTGAATTAA
* *
7507 ACTCATTCACGTGAGAATTGTTTCTCTCTTGGTTCTGGGA-TAAACTTCCAAACTTGTCAAACTT
573 ACTCATTCACGTGAGAATTGTTTCTCTCTTGGTTCTGGGACTAAACTTTCAAACTTTTCAAACTT
* * * * ** **
7571 TTT-CTTTGGTACCTTAAAGTATTCAAGATGATTCATTCCGTCGAGCAATTTTTTGAACATTCCA
638 TTTACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAAAAAAATTTTGAACATTCCA
* * * *
7635 TGCT-TGAAAAATTGTATCATTTGGTCTAAATAGATAGTCATTTTGTAAAAAAGTTTGTGTCTTT
703 TGCTCAG-AAAATTGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTGTGTCTTT
7699 GAATTAAAAACAT-ATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTG
767 GAATTAAAAAC-TCATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGA-GAA---CTG
* * * *
7758 AACGTGTCAAACTTTTATGAGTTCCTTTATAACTTTGGTTCCTCAAAGTATTTAAGGCGATCCAT
1 AACATGTCAAACTTTTA-GA--TACTTTATAACTTTGGTTCCTTAAAGTATTCAAGGCGATCCAT
* * *
7823 TCCTTTGAGCAATTTTTCGAACATTCCATGCTCAGGTAATAGAATCATTTTGTCTAAATAGTTTG
63 TCCTTTGAGCAATTTTTCGAACATTCCATGCTCGGGTAATCGAATCATTTGGTCTAAATAGTTTG
*
7888 TCATTTTGTAAACAGGTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTAT
128 TCATTTTGTAAAAAGGTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTAT
* * *
7953 TGGTTCTGGGTTAAACTTCCAAACTTGTCAAACTTTTACTAATTCTTTTATAACTTCGGTTCCTT
193 TGGTTCTGGGATGAACTTCCGAACTTGTCAAACTTTTACTAATTCTTTTATAACTTCGGTTCCTT
8018 AAAGTATTCAAGACGATGCATTCCTTCGAGCAAT---TTTCTCGAGAAATCGCATCATTTGGTCT
258 AAAGTATTCAAGACGATGCATTCCTTCGAGCAATAAATTTCTCGAGAAATCGCATCATTTGGTCT
*
8080 AAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTTAATTAAAAACTTATTTACGTGAGAATT
323 AAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATT
*
8145 GTTTCTCTTGGTTCTTGGACGAACTTAAGAAATTGTCAAACTTTTTTGAGATCTTTTATTACTTT
388 GTTTCTC----TTCTTGGA-GAACTTAAG--A--GTCAAACTTTTTCGAGATCTTTTATTACTTT
* * *
8210 GATTCCTTAAAAGTATTCAAGACGATCCATTCCATCAAAAAATTTTCTGAACATTCCATGCTAAA
444 GATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGAAAAATTTTCTGAACATTCCATGCTCAG
*
8275 AAAATTGAATCATTTTGTCT--A-A---CGTCATTTTGTAAACATGTTTTCGTCTTTGAATTAAA
509 AAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTTGTAAACATGTTTTCGTCTTTGAATTAAA
*
8334 CTCATTCACGTGAGAATTGTTTCTCTCTTGGTTCTGGGAC-AAACTTTCGAACTTGTT-AAAC-T
574 CTCATTCACGTGAGAATTGTTTCTCTCTTGGTTCTGGGACTAAACTTTCAAACTT-TTCAAACTT
* * **
8396 TTTACTTT-GTTACCTTAAAGTATTCAAGACGATCCATTTCTT--TAAGCAATTTCTCGAACATT
638 TTTACTTTGGTT-CCTTAAAGTATTCAAGACGATCCATTCCTTCGAAAAAAATTT-T-GAACATT
* * * * *
8458 TCGTGCTCAGGAAATGGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTGTGTCT
700 CCATGCTCAGAAAATTGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTGTGTCT
*
8523 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAACTTCTG
765 TTGAATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGA-GAA---CTG
* * *
8584 AACATGTCAAACTTTTACGAGTTTCTTTATAACTTTGGTTCCTCAAAGTATTTAAGGCGATCCAT
1 AACATGTCAAACTTTTA-GA--TACTTTATAACTTTGGTTCCTTAAAGTATTCAAGGCGATCCAT
* *
8649 TCCTTTGAGCAATTTTTCGAACATTTCATGCTCGGGTAATCGAATCATTTGGTCTAAATTGTTTG
63 TCCTTTGAGCAATTTTTCGAACATTCCATGCTCGGGTAATCGAATCATTTGGTCTAAATAGTTTG
*
8714 TCATTTTGTAAATAGGTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTAT
128 TCATTTTGTAAAAAGGTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTAT
* * * ** *
8779 TGGTTCTAGG-TCAAACTTCCAAACTTGTCAAACTTTTACTAATTCTTTTATAGGTTCGATTCCT
193 TGGTTCTGGGAT-GAACTTCCGAACTTGTCAAACTTTTACTAATTCTTTTATAACTTCGGTTCCT
8843 TAAAGTATTCAAGACGATGCATTCCTTCGAGC---AAATTTCTCGAGAAATCGCATCATTTGGTC
257 TAAAGTATTCAAGACGATGCATTCCTTCGAGCAATAAATTTCTCGAGAAATCGCATCATTTGGTC
8905 TAAATAGTTTGTCA-TTTCTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAAT
322 TAAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAAT
8969 TGTTTCTCTTGGTTCTTGGACGAACTTAAGAACTTGTCAAACTTTTTCGAGATCTTTTATTACTT
387 TGTTTCTC----TTCTTGGA-GAACTTAAG-A---GTCAAACTTTTTCGAGATCTTTTATTACTT
** *
9034 TGATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGAAAGTTTTTTTGAACATTCCATGCTCA
443 TGATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGAAAAATTTTCTGAACATTCCATGCTCA
* * *
9099 GAAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTAGTAAACATGTTTCCATCTTTGAATTAA
508 GAAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTTGTAAACATGTTTTCGTCTTTGAATTAA
* *
9164 ACTCATTCACGTGAGAACTGTTTCTCTCTTGGTTCTTGGACGAACTTAAGAAATTGTCAAACTTT
573 ACTCATTCACGTGAGAATTGTTTCTCTCTTGGTTC-TGG--G-AC-T-A-AACTT-TCAAACTTT
* * * *
9229 TACAAGATCCTTTATTACTTCGGTTCCTTAAAAGTATTTAAGACAATCCATTCCTTCAAAAAAAA
630 T-CAA-A--CTTT-TTACTTTGGTTCCTT-AAAGTATTCAAGACGATCCATTCCTTCGAAAAAAA
* ** * * * * *
9294 ATTTGAATGTTGCATGCTCGGGAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTTGCAAAGA
689 TTTTGAACATTCCATGCTCAGAAAATTGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-A
* * * *
9359 TATTTTG-GTCTTTGAATTAAAAACTCATTTACATGAGAATTGTTTCTCTCTTGCTTC-TGG-G-
753 AAGTTTGTGTCTTTGAATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAGA
9420 A-TG
818 ACTG
* * *
9423 AAC-TTTCAAACTTGTTA-A-ACTTT-T-ACTTTGGTACCTTAAAGTATTCAAGACGATCCATTC
1 AACATGTCAAACTT-TTAGATACTTTATAACTTTGGTTCCTTAAAGTATTCAAGGCGATCCATTC
** * ** * *
9483 CTTTGAGCAATTTCCCAAACATTCCGA-GCTCAAGAAATCGCATCATTTGGTCTAAATAGTTTGT
65 CTTTGAGCAATTTTTCGAACATTCC-ATGCTCGGGTAATCGAATCATTTGGTCTAAATAGTTTGT
* * * * *
9547 CATTTTGTAAAAAAG-TTTGTGTCTTTGAATTAAAAATTTATTTACGTGAGAATTGTTTCTCTCT
129 CATTTTGTAAAAAGGTTTTG-GTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTAT
* * * * * * * *
9611 TGGTTCTTGGATGAACTTCTGAACATGTCAAACTTTTACGAGTTCCTTTATAACTTTGGTTCCTC
193 TGGTTCTGGGATGAACTTCCGAACTTGTCAAACTTTTACTAATTCTTTTATAACTTCGGTTCCTT
* * * * * * *
9676 AAAGTATTTAAGGCGATCCATTCCTTTGAGCAATTTTTTGAACATTCCATGCTCGGGTAATCGAA
258 AAAGTATTCAAGACGATGCATTCCTTCGAGCAA-----T-AA-ATT---T-CTCGAGAAATCGCA
* *
9741 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAGGTTTTGGTCTTTAAATTAAAAACTTATTT
312 TCATTTGGTCTAAATAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATTT
** * * *
9806 ATATGAGAATTGTTTCTC-TATTGGTTCTAGGTCAAACTTCCAA-ACTTGTCAAACTTTTACTA-
377 ACGTGAGAATTGTTTCTCTTCTTGG----A-G---AACTT--AAGA---GTCAAACTTTTTCGAG
* * * * * * **
9868 ATTCTTTTATAACTTCGGTTCC-TAAAAGTATTCAAGATGATACATTCCTTCGAGCAA-TTT-T-
429 A-TCTTTTATTACTTTGATTCCTTAAAAGTATTCAAGACGATCCATTCCATCGAAAAATTTTCTG
* * * * *
9929 --C--T-C--G---AG-AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTCTAAACAAGTTT
493 AACATTCCATGCTCAGAAAATTGAATCATTTTGTCTAAATAGTTTGTCATTTTGTAAACATGTTT
* * * *
9983 TGGTCTTTTAATTAAAAACTTATTTACGTGAGAATTG-TT-TCTCTTGGTTCTTGGACGAACTTA
558 TCGTCTTTGAATT--AAACTCATTCACGTGAGAATTGTTTCTCTCTTGGTTC-TGG--G-AC-T-
* *
10046 AGAACTTGTCAAACTTTTTCGAGATCCTTTATTACTTTGATTCCTTAAAAGTATTCAAGACGATC
615 A-AACTT-TCAAAC-TTTTC-A-A-ACTTT-TTACTTTGGTTCCTT-AAAGTATTCAAGACGATC
* **** *
10111 CATTCCATCGAAAGTTCTTTTGAACATTCCATGCTCAGAAAATTGAATCATTTTGTCTAAATAGT
672 CATTCCTTCGAAAAAAATTTTGAACATTCCATGCTCAGAAAATTGAATCATTTGGTCTAAATAGT
* * * * *
10176 TTGTCATTTAGTAAACATGTTT-TCGTCTTTGAATT--AAACTCATTCACGTGAGAACTGTTTCT
737 TTGTCATTTTGTAAAAAAGTTTGT-GTCTTTGAATTAAAAACTCATTTACGTGAGAATTGTTTCT
10238 CTCTTGGTTCTTGGATGAACTTAAG
801 CTCTTGGTTCTTGGA-GAAC-T--G
* * * * *
10263 AACTTGTCAAACTTTTACGAGATCCTTTATTACTTCGGTTCCTTAAAAGTATTCAAGACGATCCA
1 AACATGTCAAACTTTT---AGATACTTTATAACTTTGGTTCCTT-AAAGTATTCAAGGCGATCCA
** ** * ** * * * *
10328 TTCCTTCAAAAAAAATTTT-GAATGTTGCATGCTCGGGAAATTGAATCATTTTGTCTAAATAGTT
62 TTCCTT-TGAGCAATTTTTCGAACATTCCATGCTCGGGTAATCGAATCATTTGGTCTAAATAGTT
* * ** * * *
10392 TGTCATTTTGCAAAGATATTTTGGTCTGTGAATTAAAAACTCATTTATGTGAGAATTGTTTCTCT
126 TGTCATTTTGTAAAAAGGTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCT
* *
10457 CTTGGTTCTGGGACGAACTTCCGAACTTGTCAAACTTTTACT
191 ATTGGTTCTGGGATGAACTTCCGAACTTGTCAAACTTTTACT
10499 TTGGTACCTT
Statistics
Matches: 2403, Mismatches: 239, Indels: 181
0.85 0.08 0.06
Matches are distributed among these distances:
824 5 0.00
825 199 0.08
826 557 0.23
827 3 0.00
828 1 0.00
829 1 0.00
830 1 0.00
831 191 0.08
832 632 0.26
833 12 0.00
834 206 0.09
835 12 0.00
836 21 0.01
837 1 0.00
838 12 0.00
839 14 0.01
840 14 0.01
841 14 0.01
842 9 0.00
843 3 0.00
844 3 0.00
845 7 0.00
846 52 0.02
847 192 0.08
848 185 0.08
849 54 0.02
851 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (821 bp):
AACATGTCAAACTTTTAGATACTTTATAACTTTGGTTCCTTAAAGTATTCAAGGCGATCCATTCC
TTTGAGCAATTTTTCGAACATTCCATGCTCGGGTAATCGAATCATTTGGTCTAAATAGTTTGTCA
TTTTGTAAAAAGGTTTTGGTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTATTGG
TTCTGGGATGAACTTCCGAACTTGTCAAACTTTTACTAATTCTTTTATAACTTCGGTTCCTTAAA
GTATTCAAGACGATGCATTCCTTCGAGCAATAAATTTCTCGAGAAATCGCATCATTTGGTCTAAA
TAGTTTGTCATTTTCTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTT
TCTCTTCTTGGAGAACTTAAGAGTCAAACTTTTTCGAGATCTTTTATTACTTTGATTCCTTAAAA
GTATTCAAGACGATCCATTCCATCGAAAAATTTTCTGAACATTCCATGCTCAGAAAATTGAATCA
TTTTGTCTAAATAGTTTGTCATTTTGTAAACATGTTTTCGTCTTTGAATTAAACTCATTCACGTG
AGAATTGTTTCTCTCTTGGTTCTGGGACTAAACTTTCAAACTTTTCAAACTTTTTACTTTGGTTC
CTTAAAGTATTCAAGACGATCCATTCCTTCGAAAAAAATTTTGAACATTCCATGCTCAGAAAATT
GAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTGTGTCTTTGAATTAAAAACTCA
TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAGAACTG
Found at i:10414 original size:21 final size:21
Alignment explanation
Indices: 10373--10414 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
10363 GGAAATTGAA
*
10373 TCATTTTGTCTAAATAGTTTG
1 TCATTTTGTCAAAATAGTTTG
*
10394 TCATTTTG-CAAAGATATTTTG
1 TCATTTTGTCAAA-ATAGTTTG
10415 GTCTGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (21 bp):
TCATTTTGTCAAAATAGTTTG
Found at i:12628 original size:18 final size:18
Alignment explanation
Indices: 12605--12641 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12595 TCTTAAGAGC
*
12605 ATTCTGTCCCCATTTAGA
1 ATTCTGACCCCATTTAGA
*
12623 ATTCTGACTCCATTTAGA
1 ATTCTGACCCCATTTAGA
12641 A
1 A
12642 GTAGAAGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (18 bp):
ATTCTGACCCCATTTAGA
Found at i:14433 original size:74 final size:74
Alignment explanation
Indices: 14338--14487 Score: 273
Period size: 74 Copynumber: 2.0 Consensus size: 74
14328 CTTTACAAAA
14338 TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATGTGTTAATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATGTGTTAATTCATTTAAAAACTCTTGA
14403 ATGAAACAT
66 ATGAAACAT
* * *
14412 TGAATGTGAACAGCCATCATTCATCATTCATAAATGAATGTGTTGATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATGTGTTAATTCATTTAAAAACTCTTGA
14477 ATGAAACAT
66 ATGAAACAT
14486 TG
1 TG
14488 TATCCCTCCA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (74 bp):
TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATGTGTTAATTCATTTAAAAACTCTTGA
ATGAAACAT
Found at i:14760 original size:2 final size:2
Alignment explanation
Indices: 14749--14782 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
14739 ATTGTACCTT
14749 AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
14783 TATATAAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15633 original size:215 final size:215
Alignment explanation
Indices: 15262--15858 Score: 670
Period size: 215 Copynumber: 2.8 Consensus size: 215
15252 TGAATTTTTG
* * * *
15262 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAATTATTGAAGACGATCCAT
1 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCC-TAAAGTATTCAAGATGATCCAT
** * * * * *
15327 TCCTTTGAGTAATTTCTCAAACATTCCGTGCTCGAGAAATTGCATCATTTGGTCTAAATAGTTTT
65 TCCTTCAAGTAATTTCTCAAACATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATAGTTTG
* * * *
15392 TCATTTTGTTATCAACCTTTGGTCTTTGAATTAAAAACTTATTTACATTAGAATTG-TTCTCTCT
130 TCATTTTGTAAACAAACTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCT
**
15456 TGGTTCTTGGATGAACTTCCA
195 TGGTTCTTGGACAAACTTCCA
* *
15477 AACTTGTTAAACTTTTACGAGTTCTTTTATAAATTCGGTTCCTCAAAGTATTCAAGATGATCCAT
1 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCT-AAAGTATTCAAGATGATCCAT
* ** *
15542 T-CTCTCAAGCT-ATTTTTTGAATATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATAGTT
65 TCCT-TCAAG-TAATTTCTCAAACATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATAGTT
* ** *
15605 TGTCATTTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTTT
128 TGTCATTTTGTAAACAAACTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCT
* *
15670 CTTGGTTGTTGGACAAACTTCCG
193 CTTGGTTCTTGGACAAACTTCCA
* *
15693 AACATGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCATAAAGTATTCAAGATGATCCAT
1 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCC-TAAAGTATTCAAGATGATCCAT
* * **
15758 TCCTTCGAGCAATTT-T----C--T-C-TG-----GAAATATCATCATTTGGTCTAAATAGTTTG
65 TCCTTCAAGTAATTTCTCAAACATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATAGTTTG
* ** * *
15809 TCATTTTCTAAACAAGTTTTGGTATTTGAATTAAAAACGTATTTACATGA
130 TCATTTTGTAAACAAACTTTGGTCTTTGAATTAAAAACTTATTTACATGA
15859 TGCGAGCACG
Statistics
Matches: 331, Mismatches: 44, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
202 72 0.22
207 2 0.01
208 1 0.00
209 1 0.00
214 3 0.01
215 156 0.47
216 93 0.28
217 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.42
Consensus pattern (215 bp):
AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTAAAGTATTCAAGATGATCCATT
CCTTCAAGTAATTTCTCAAACATTCCATGCACAAGAAATCGCATCATTTGGTCTAAATAGTTTGT
CATTTTGTAAACAAACTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTT
GGTTCTTGGACAAACTTCCA
Found at i:15879 original size:15 final size:15
Alignment explanation
Indices: 15858--15896 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
15848 TATTTACATG
*
15858 ATGCGAGCACGAGTA
1 ATGCGAGCACGAATA
* *
15873 GTGCGAGCACTAATA
1 ATGCGAGCACGAATA
15888 ATGCGAGCA
1 ATGCGAGCA
15897 TGGAAGATGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.31, T:0.15
Consensus pattern (15 bp):
ATGCGAGCACGAATA
Found at i:23021 original size:50 final size:50
Alignment explanation
Indices: 22947--23077 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
22937 TGCATAACTT
22947 GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAA-TTTAACTAACATGGAAGTTACATAATGCATG-TCAG
* * * *
22999 GATTTATGATGCATATTTAACTAACATGTAAGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
* *
23049 TATTTATGATGCAAACTTAACTAATCATG
1 GATTTATGATGCAAATTTAACTAA-CATG
23078 AGAGTTANNN
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 1 0.01
50 51 0.73
51 13 0.19
52 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (50 bp):
GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
Found at i:23369 original size:50 final size:50
Alignment explanation
Indices: 23295--23425 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
23285 TGCATAACTT
23295 GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAA-TTTAACTAACATGGAAGTTACATAATGCATG-TCAG
* * * *
23347 GATTTATGATGCATATTTAACTAACATGTAAGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
* *
23397 TATTTATGATGCAAACTTAACTAATCATG
1 GATTTATGATGCAAATTTAACTAA-CATG
23426 AGAGTTAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 1 0.01
50 51 0.73
51 13 0.19
52 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (50 bp):
GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
Found at i:23531 original size:33 final size:34
Alignment explanation
Indices: 23467--23531 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
23457 ACTTTATTAA
* * *
23467 ATGTAGATCACATAATGTATGTCATATTTAAAAG
1 ATGTAGATCACATAATGCATGACATAATTAAAAG
*
23501 ATGTAGATTA-ATAATGCATGACATAATTAAA
1 ATGTAGATCACATAATGCATGACATAATTAAA
23532 TCACAATCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.34
Consensus pattern (34 bp):
ATGTAGATCACATAATGCATGACATAATTAAAAG
Found at i:23651 original size:16 final size:17
Alignment explanation
Indices: 23630--23662 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
23620 ACACTTATTA
23630 AAATAAAA-TAAAAATT
1 AAATAAAATTAAAAATT
23646 AAATAAAATTAAAAATT
1 AAATAAAATTAAAAATT
23663 CCTTCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAAATTAAAAATT
Found at i:24968 original size:216 final size:216
Alignment explanation
Indices: 24562--25871 Score: 1271
Period size: 216 Copynumber: 6.2 Consensus size: 216
24552 GAGAAATGTT
** * * * *
24562 TCTCTTGGTTCTTTGACGAACTTAAGAACTTGTCAAACTTTTATGAGATCCTTTATTACTTCGGT
1 TCTCTTGGTTCTGGGACGAACTTACGAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGT
* * * ** * *
24627 TCTTTAAAAGTATTCAAGACAATCCATTCCTTCGA-AAATTTACCGAACATTCCTTGCTCGGGAA
66 TCCTT-AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAA
* * * * *
24691 ATTGAATCATTTTGTCTAAATAGTTTGCCATTTTGTAAAGATGTTTTGGTC-TTAGAATTAAAAA
130 ATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTA-AATTAAAAA
24755 CTCATTTACGTGAGAATTGTTTC
194 CTCATTTACGTGAGAATTGTTTC
* * * * * *
24778 TCTTTTGATTCTAGGACGAACTTCCGAACTTGTTAAACTTTTACGAGTTCCTTTATAACTTTGGT
1 TCTCTTGGTTCTGGGACGAACTTACGAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGT
* * * * **
24843 TCCTTAAACTATTCAAAATGATTCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGTTA
66 TCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAA
* * * * * *
24908 TCGAATCATTTGGTCAAAATAGTTTGCCATTTTCTAAACAGGTTTTCGTCTTTAAATTAAAAAGT
131 TCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAAACT
* *
24973 TATTTATGTGAGAATTGTTTC
196 CATTTACGTGAGAATTGTTTC
* * * * * * *
24994 TCTATTGATTCTGGGAAGAACTTTCGAACTTATCAAACTTTTACTAGTTCTTTTATAACTTCGGT
1 TCTCTTGGTTCTGGGACGAACTTACGAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGT
* * *
25059 ACCTTAAAGTATTCAAGACGATGCATTCCTTCAAGCAA----T------TT---T-CTCGAGAAA
66 TCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAA
* * * ** *
25110 TTGCATCATTTGGTCTAAATAGTTTTTCATTTCCTAAACAAGTTTTGGTCTTTTAATTAAAAACT
131 TCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAAACT
*
25175 TATTTACGTGAGAATTGTTT-
196 CATTTACGTGAGAATTGTTTC
* * ** * *
25195 T-TCTTGGTTCTCGGACGAACTTAAGAACTTGTCAAACTATTT-TTAGATCCTTTATTACTTCGG
1 TCTCTTGGTTCTGGGACGAACTTACGAACTTGTCAAACT-TTTACGAGTTCCTTTATAACTTCGG
* * * *
25258 TTCCTTAAAAGTATTCAAGACGATCCATTCCTTC-A-AAAATTTTCTACACATTCCATGCTCGGG
65 TTCCTT-AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGA-ACATTCCATGCTCGAG
* * * * * *
25321 AAATTGAATCATTTTGTCTAAATAGTTTGTCAATTTGTAAACATGTTTTGGCCTTTGAATTAAAA
128 AAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAA
25386 ACTCATTTACGTGAGAATTGTTTC
193 ACTCATTTACGTGAGAATTGTTTC
* ** * * *
25410 TCTCTTGGTCCTGGGATAAACTTTCAAACTTGCCAAACTTTT---A----C-TT-T-A-----GT
1 TCTCTTGGTTCTGGGACGAACTTACGAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGT
* * * * *
25460 ACCTTAAACTATTCAAGACGATCCATTCCGTT-GAGCAATTTTTTGAACATTCCACGCTCGAAAA
66 TCCTTAAAGTATTCAAGACGATCCATTCC-TTCGAGCAATTTTTCGAACATTCCATGCTCGAGAA
* * *
25524 ATC-ACATCAATTGGTCTAAATAGTTTGTCATTTTGTAAAAAAG-TTTGTGTCTTTGAATTAAAA
130 ATCGA-ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTG-GTCTTTAAATTAAAA
* * *
25587 ACTTATTTATGTGAGAACTGTTTC
193 ACTCATTTACGTGAGAATTGTTTC
* * * * *
25611 TCTCTTGGTTCTTGGACGAACTTTCGAACTCGTAAAACTTTTTATGAGTT-CTGTTATAACTTCG
1 TCTCTTGGTTCTGGGACGAACTTACGAACTTGTCAAAC-TTTTACGAGTTCCT-TTATAACTTCG
* * * *
25675 GTTCCTTAAAGTATTTAAGACAATCCATTCCTTTGAGCAAATTTTT-GAACATTCCATGCTTGAG
64 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGC-AATTTTTCGAACATTCCATGCTCGAG
* * * *
25739 TAATCGAATCATTTGGTCTAAATAGTTTGACATTTTGTAAATAGGTTTTGGTCTTTAAATTTAAA
128 AAATCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAA-TT-AA
25804 AAACTCATTTACGTGAGAATTGTTTC
191 AAACTCATTTACGTGAGAATTGTTTC
* * * *
25830 TCTCTTGGTTTTGGGATGAACTTCCGAACTTGTCAAATTTTT
1 TCTCTTGGTTCTGGGACGAACTTACGAACTTGTCAAACTTTT
25872 TGATGTGAGC
Statistics
Matches: 901, Mismatches: 145, Indels: 94
0.79 0.13 0.08
Matches are distributed among these distances:
199 2 0.00
200 81 0.09
201 154 0.17
202 92 0.10
203 2 0.00
205 1 0.00
206 3 0.00
207 1 0.00
208 3 0.00
209 1 0.00
210 4 0.00
211 1 0.00
212 2 0.00
213 2 0.00
214 83 0.09
215 28 0.03
216 272 0.30
217 95 0.11
218 18 0.02
219 56 0.06
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (216 bp):
TCTCTTGGTTCTGGGACGAACTTACGAACTTGTCAAACTTTTACGAGTTCCTTTATAACTTCGGT
TCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAA
TCGAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAAACT
CATTTACGTGAGAATTGTTTC
Found at i:25789 original size:632 final size:629
Alignment explanation
Indices: 24551--25871 Score: 1589
Period size: 632 Copynumber: 2.1 Consensus size: 629
24541 CATAATTATC
* * **
24551 TGAGAAATGTTTCTCTTGGTTCTTTGACGAACTTAAGAACTTGTCAAACTTTTATGAGATCCTTT
1 TGAGAATTGTTTTTCTTGGTTCTCGGACGAACTTAAGAACTTGTCAAACTTTTATGAGATCCTTT
* * *
24616 ATTACTTCGGTTCTTTAAAAGTATTCAAGACAATCCATTCCTTCGAAAATTTACCGAACATTCCT
66 ATTACTTCGGTTCCTTAAAAGTATTCAAGACAATCCATTCCTTCAAAAATTTACCGAACATTCCA
* * *
24681 TGCTCGGGAAATTGAATCATTTTGTCTAAATAGTTTGCCATTTTGTAAAGATGTTTTGGTCTTAG
131 TGCTCGGGAAATTGAATCATTTTGTCTAAATAGTTTGCCAATTTGTAAACATGTTTTGGCCTTAG
* * *
24746 AATTAAAAACTCATTTACGTGAGAATTGTTTCTCTTTTGATTCTAGGACGAACTTCCGAACTTGT
196 AATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGATCCTAGGA-GAAC-T-CAAACTTGT
* * ** * * * *
24811 TAAACTTTTACGAGTTCCTTTATAACTTTGGTTCCTTAAACTATTCAAAATGATTCATTCCTTCG
258 CAAAC-TTTACCAG-AACTTTATAACTTTAGTACCTTAAACTATTCAAAACGATCCATTCCTTCG
* *** *
24876 AGCAATTTTTCGAACATTCCATGCTCGAGTTATCGAATCATTTGGTCAAAATAGTTTGCCATTTT
321 AGCAATTTTTCGAACATTCCACGCTCGAAAAATCGAATCAATTGGTCAAAATAGTTTGCCATTTT
* * * *
24941 CTAAACAGGTTTTCGTCTTTAAATTAAAAAGTTATTTATGTGAGAATTGTTTCTCTATTGATTCT
386 CTAAAAAAGTTTTCGTCTTTAAATTAAAAACTTATTTATGTGAGAACTGTTTCTCTATTGATTCT
* * *
25006 GGGAAGAACTTTCGAACTTATCAAACTTTTACTAGTTCTTTTATAACTTCGGTACCTTAAAGTAT
451 GGGAAGAACTTTCGAACTCATAAAACTTTTACTAGTTCTGTTATAACTTCGGTACCTTAAAGTAT
* * * * *
25071 TCAAGACGATGCATTCCTTCAAGCAATTTTCTCGAGAAATTGCATCATTTGGTCTAAATAGTTTT
516 TCAAGACAATCCATTCCTTCAAGCAATTTTCTCGAGAAATCGAATCATTTGGTCTAAATAGTTTG
* * *
25136 TCATTTCCTAAACAAGTTTTGGTCTTTTAA-TT-AAAAACTTATTTACG
581 ACATTTCCTAAACAAGTTTTGGTCTTTAAATTTAAAAAACTCATTTACG
*
25183 TGAGAATTGTTTTTCTTGGTTCTCGGACGAACTTAAGAACTTGTCAAACTATTT-TTAGATCCTT
1 TGAGAATTGTTTTTCTTGGTTCTCGGACGAACTTAAGAACTTGTCAAACT-TTTATGAGATCCTT
* * *
25247 TATTACTTCGGTTCCTTAAAAGTATTCAAGACGATCCATTCCTTCAAAAATTT-TCTACACATTC
65 TATTACTTCGGTTCCTTAAAAGTATTCAAGACAATCCATTCCTTCAAAAATTTACCGA-ACATTC
*
25311 CATGCTCGGGAAATTGAATCATTTTGTCTAAATAGTTTGTCAATTTGTAAACATGTTTTGGCCTT
129 CATGCTCGGGAAATTGAATCATTTTGTCTAAATAGTTTGCCAATTTGTAAACATGTTTTGGCCTT
* *
25376 TGAATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGGTCCT-GG-G-A-T-AAACTT-TC
194 AGAATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGATCCTAGGAGAACTCAAACTTGTC
* *
25435 AAAC-TTGCCA-AACTTT-T-ACTTTAGTACCTTAAACTATTCAAGACGATCCATTCCGTT-GAG
259 AAACTTTACCAGAACTTTATAACTTTAGTACCTTAAACTATTCAAAACGATCCATTCC-TTCGAG
* * * *
25495 CAATTTTTTGAACATTCCACGCTCGAAAAATC-ACATCAATTGGTCTAAATAGTTTGTCATTTTG
323 CAATTTTTCGAACATTCCACGCTCGAAAAATCGA-ATCAATTGGTCAAAATAGTTTGCCATTTTC
* * *
25559 TAAAAAAGTTTGT-GTCTTTGAATTAAAAACTTATTTATGTGAGAACTGTTTCTCTCTTGGTTCT
387 TAAAAAAGTTT-TCGTCTTTAAATTAAAAACTTATTTATGTGAGAACTGTTTCTCTATTGATTCT
* * * *
25623 TGGACGAACTTTCGAACTCGTAAAACTTTTTA-TGAGTTCTGTTATAACTTCGGTTCCTTAAAGT
451 GGGAAGAACTTTCGAACTCATAAAAC-TTTTACT-AGTTCTGTTATAACTTCGGTACCTTAAAGT
* ** *
25687 ATTTAAGACAATCCATTCCTTTGAGCAAATTTTTGAACATTCCATGCTTGAGTAATCGAATCATT
514 ATTCAAGACAATCCATTCCTTCAAGC-AA---TT-----TT-C-T-C--GAGAAATCGAATCATT
** * *
25752 TGGTCTAAATAGTTTGACATTTTGTAAATAGGTTTTGGTCTTTAAATTTAAAAAACTCATTTACG
565 TGGTCTAAATAGTTTGACATTTCCTAAACAAGTTTTGGTCTTTAAATTTAAAAAACTCATTTACG
* * * ** *
25817 TGAGAATTGTTTCTCTCTTGGTTTTGGGATGAACTTCCGAACTTGTCAAATTTTT
1 TGAGAATTGTTT-T-TCTTGGTTCTCGGACGAACTTAAGAACTTGTCAAACTTTT
25872 TGATGTGAGC
Statistics
Matches: 589, Mismatches: 75, Indels: 47
0.83 0.11 0.07
Matches are distributed among these distances:
616 1 0.00
617 165 0.28
618 58 0.10
619 6 0.01
621 4 0.01
622 2 0.00
623 5 0.01
624 5 0.01
626 1 0.00
627 2 0.00
628 2 0.00
629 2 0.00
630 1 0.00
631 4 0.01
632 265 0.45
633 5 0.01
634 26 0.04
635 4 0.01
636 31 0.05
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (629 bp):
TGAGAATTGTTTTTCTTGGTTCTCGGACGAACTTAAGAACTTGTCAAACTTTTATGAGATCCTTT
ATTACTTCGGTTCCTTAAAAGTATTCAAGACAATCCATTCCTTCAAAAATTTACCGAACATTCCA
TGCTCGGGAAATTGAATCATTTTGTCTAAATAGTTTGCCAATTTGTAAACATGTTTTGGCCTTAG
AATTAAAAACTCATTTACGTGAGAATTGTTTCTCTCTTGATCCTAGGAGAACTCAAACTTGTCAA
ACTTTACCAGAACTTTATAACTTTAGTACCTTAAACTATTCAAAACGATCCATTCCTTCGAGCAA
TTTTTCGAACATTCCACGCTCGAAAAATCGAATCAATTGGTCAAAATAGTTTGCCATTTTCTAAA
AAAGTTTTCGTCTTTAAATTAAAAACTTATTTATGTGAGAACTGTTTCTCTATTGATTCTGGGAA
GAACTTTCGAACTCATAAAACTTTTACTAGTTCTGTTATAACTTCGGTACCTTAAAGTATTCAAG
ACAATCCATTCCTTCAAGCAATTTTCTCGAGAAATCGAATCATTTGGTCTAAATAGTTTGACATT
TCCTAAACAAGTTTTGGTCTTTAAATTTAAAAAACTCATTTACG
Found at i:27082 original size:50 final size:51
Alignment explanation
Indices: 27008--27123 Score: 155
Period size: 50 Copynumber: 2.3 Consensus size: 51
26998 TGCATAACTT
27008 GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATG-TCAG
* * * *
27060 GATTTATGATGCATA-TTTAACTAACATGTAAGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGTCAG
*
27110 TATTTATGATGCAA
1 GATTTATGATGCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 1 0.02
50 42 0.74
51 9 0.16
52 5 0.09
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (51 bp):
GATTTATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGTCAG
Done.